Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica)
Abstract Background Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecu...
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| Format: | Article |
| Language: | English |
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BMC
2021-09-01
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| Series: | Plant Methods |
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| Online Access: | https://doi.org/10.1186/s13007-021-00792-9 |
| _version_ | 1819115238871531520 |
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| author | Haiyan Wang Jiangbo Dang Di Wu Zhongyi Xie Shuang Yan Jingnan Luo Qigao Guo Guolu Liang |
| author_facet | Haiyan Wang Jiangbo Dang Di Wu Zhongyi Xie Shuang Yan Jingnan Luo Qigao Guo Guolu Liang |
| author_sort | Haiyan Wang |
| collection | DOAJ |
| description | Abstract Background Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecular breeding. Results We developed a system for genotyping by quantitative PCR (qPCR) that allowed flesh color genotyping in multiple tetraploid and triploid loquat varieties (lines). The analysis of 13 different ratios of DNA mixtures between two homozygous diploids (AA and aa) showed that the proportion of allele A has a high correlation (R2 = 0.9992) with parameter b [b = a1/(a1 + a2)], which is derived from the two normalized allele signals (a1 and a2) provided by qPCR. Cluster analysis and variance analysis from simulating triploid and tetraploid hybrids provided completely correct allelic configurations. Four genotypes (AAA, AAa, Aaa, aaa) were found in triploid loquats, and four (AAAA, AAAa, AAaa, Aaaa; absence of aaaa homozygotes) were found in tetraploid loquats. DNA markers analysis showed that the segregation of flesh color in all F1 hybrids conformed to Mendel's law. When tetraploid B431 was the female parent, more white-fleshed triploids occurred among the progeny. Conclusions qPCR can detect the flesh color genotypes of loquat polyploids and provides an alternative method for analyzing polyploid genotype and breeding, dose effects and allele-specific expression. |
| first_indexed | 2024-12-22T04:58:01Z |
| format | Article |
| id | doaj.art-f617f0cb786849009987222719573620 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-12-22T04:58:01Z |
| publishDate | 2021-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-f617f0cb7868490099872227195736202022-12-21T18:38:20ZengBMCPlant Methods1746-48112021-09-0117111810.1186/s13007-021-00792-9Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica)Haiyan Wang0Jiangbo Dang1Di Wu2Zhongyi Xie3Shuang Yan4Jingnan Luo5Qigao Guo6Guolu Liang7Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest UniversityKey Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest UniversityKey Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest UniversityKey Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest UniversityKey Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest UniversityKey Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest UniversityKey Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest UniversityKey Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest UniversityAbstract Background Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecular breeding. Results We developed a system for genotyping by quantitative PCR (qPCR) that allowed flesh color genotyping in multiple tetraploid and triploid loquat varieties (lines). The analysis of 13 different ratios of DNA mixtures between two homozygous diploids (AA and aa) showed that the proportion of allele A has a high correlation (R2 = 0.9992) with parameter b [b = a1/(a1 + a2)], which is derived from the two normalized allele signals (a1 and a2) provided by qPCR. Cluster analysis and variance analysis from simulating triploid and tetraploid hybrids provided completely correct allelic configurations. Four genotypes (AAA, AAa, Aaa, aaa) were found in triploid loquats, and four (AAAA, AAAa, AAaa, Aaaa; absence of aaaa homozygotes) were found in tetraploid loquats. DNA markers analysis showed that the segregation of flesh color in all F1 hybrids conformed to Mendel's law. When tetraploid B431 was the female parent, more white-fleshed triploids occurred among the progeny. Conclusions qPCR can detect the flesh color genotypes of loquat polyploids and provides an alternative method for analyzing polyploid genotype and breeding, dose effects and allele-specific expression.https://doi.org/10.1186/s13007-021-00792-9qPCR genotypingPolyploidFlesh colorAllele dosagePolyploid breedingLoquat |
| spellingShingle | Haiyan Wang Jiangbo Dang Di Wu Zhongyi Xie Shuang Yan Jingnan Luo Qigao Guo Guolu Liang Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica) Plant Methods qPCR genotyping Polyploid Flesh color Allele dosage Polyploid breeding Loquat |
| title | Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica) |
| title_full | Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica) |
| title_fullStr | Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica) |
| title_full_unstemmed | Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica) |
| title_short | Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica) |
| title_sort | genotyping of polyploid plants using quantitative pcr application in the breeding of white fleshed triploid loquats eriobotrya japonica |
| topic | qPCR genotyping Polyploid Flesh color Allele dosage Polyploid breeding Loquat |
| url | https://doi.org/10.1186/s13007-021-00792-9 |
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